Integrating Deep Learning and Synthetic Biology: A Co-Design Approach for Enhancing Gene Expression via N-terminal Coding Sequences

N-terminal coding sequence (NCS) influences gene expression by impacting the translation initiation rate. The NCS optimization problem is to find an NCS that maximizes gene expression. The problem is important in genetic engineering. However, current methods for NCS optimization such as rational design and statistics-guided approaches are labor-intensive yield only relatively small improvements. This paper introduces a deep learning/synthetic biology co-designed few-shot training workflow for NCS optimization. Our method utilizes k-nearest encoding followed by word2vec to encode the NCS, then performs feature extraction using attention mechanisms, before constructing a time-series network for predicting gene expression intensity, and finally a direct search algorithm identifies the optimal NCS with limited training data. We took green fluorescent protein (GFP) expressed by Bacillus subtilis as a reporting protein of NCSs, and employed the fluorescence enhancement factor as the metric of NCS optimization. Within just six iterative experiments, our model generated an NCS (MLD62) that increased average GFP expression by 5.41-fold, outperforming the state-of-the-art NCS designs. Extending our findings beyond GFP, we showed that our engineered NCS (MLD62) can effectively boost the production of N-acetylneuraminic acid by enhancing the expression of the crucial rate-limiting GNA1 gene, demonstrating its practical utility. We have open-sourced our NCS expression database and experimental procedures for public use.

HyperSNN: A new efficient and robust deep learning model for resource constrained control applications

In light of the increasing adoption of edge computing in areas such as intelligent furniture, robotics, and smart homes, this paper introduces HyperSNN, an innovative method for control tasks that uses spiking neural networks (SNNs) in combination with hyperdimensional computing. HyperSNN substitutes expensive 32-bit floating point multiplications with 8-bit integer additions, resulting in reduced energy consumption while enhancing robustness and potentially improving accuracy. Our model was tested on AI Gym benchmarks, including Cartpole, Acrobot, MountainCar, and Lunar Lander. HyperSNN achieves control accuracies that are on par with conventional machine learning methods but with only 1.36% to 9.96% of the energy expenditure. Furthermore, our experiments showed increased robustness when using HyperSNN. We believe that HyperSNN is especially suitable for interactive, mobile, and wearable devices, promoting energy-efficient and robust system design. Furthermore, it paves the way for the practical implementation of complex algorithms like model predictive control (MPC) in real-world industrial scenarios.

Improve Long-term Memory Learning Through Rescaling the Error Temporally

This paper studies the error metric selection for long-term memory learning in sequence modelling. We examine the bias towards short-term memory in commonly used errors, including mean absolute/squared error. Our findings show that all temporally positive-weighted errors are biased towards short-term memory in learning linear functionals. To reduce this bias and improve long-term memory learning, we propose the use of a temporally rescaled error. In addition to reducing the bias towards short-term memory, this approach can also alleviate the vanishing gradient issue. We conduct numerical experiments on different long-memory tasks and sequence models to validate our claims. Numerical results confirm the importance of appropriate temporally rescaled error for effective long-term memory learning. To the best of our knowledge, this is the first work that quantitatively analyzes different errors' memory bias towards short-term memory in sequence modelling.

Efficient Hyperdimensional Computing

Hyperdimensional computing (HDC) uses binary vectors of high dimensions to perform classification. Due to its simplicity and massive parallelism, HDC can be highly energy-efficient and well-suited for resource-constrained platforms. However, in trading off orthogonality with efficiency, hypervectors may use tens of thousands of dimensions. In this paper, we will examine the necessity for such high dimensions. In particular, we give a detailed theoretical analysis of the relationship among dimensions of hypervectors, accuracy, and orthogonality. The main conclusion of this study is that a much lower dimension, typically less than 100, can also achieve similar or even higher detecting accuracy compared with other state-of-the-art HDC models. Based on this insight, we propose a suite of novel techniques to build HDC models that use binary hypervectors of dimensions that are orders of magnitude smaller than those found in the state-of-the-art HDC models, yet yield equivalent or even improved accuracy and efficiency. For image classification, we achieved an HDC accuracy of 96.88\% with a dimension of only 32 on the MNIST dataset. We further explore our methods on more complex datasets like CIFAR-10 and show the limits of HDC computing.

Low Latency Conversion of Artificial Neural Network Models to Rate-encoded Spiking Neural Networks

Spiking neural networks (SNNs) are well suited for resource-constrained applications as they do not need expensive multipliers. In a typical rate-encoded SNN, a series of binary spikes within a globally fixed time window is used to fire the neurons. The maximum number of spikes in this time window is also the latency of the network in performing a single inference, as well as determines the overall energy efficiency of the model. The aim of this paper is to reduce this while maintaining accuracy when converting ANNs to their equivalent SNNs. The state-of-the-art conversion schemes yield SNNs with accuracies comparable with ANNs only for large window sizes. In this paper, we start with understanding the information loss when converting from pre-existing ANN models to standard rate-encoded SNN models. From these insights, we propose a suite of novel techniques that together mitigate the information lost in the conversion, and achieve state-of-art SNN accuracies along with very low latency. Our method achieved a Top-1 SNN accuracy of 98.73% (1 time step) on the MNIST dataset, 76.38% (8 time steps) on the CIFAR-100 dataset, and 93.71% (8 time steps) on the CIFAR-10 dataset. On ImageNet, an SNN accuracy of 75.35%/79.16% was achieved with 100/200 time steps.